-
1
-
-
0035582244
-
An automated multidimensional protein identification technology for shotgun proteomics
-
Wolters, D. A., Washburn, M. P., and Yates, J. R. 3rd (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690.
-
(2001)
Anal. Chem
, vol.73
, pp. 5683-5690
-
-
Wolters, D.A.1
Washburn, M.P.2
Yates, J.R.3
-
2
-
-
0037435030
-
Mass spectrometry-based proteomics
-
Aebersold, R., and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207.
-
(2003)
Nature
, vol.422
, pp. 198-207
-
-
Aebersold, R.1
Mann, M.2
-
3
-
-
84871297843
-
Next-generation proteomics: Towards an integrative view of proteome dynamics
-
Altelaar, A. F., Munoz, J., and Heck, A. J. (2013) Next-generation proteomics: Towards an integrative view of proteome dynamics. Nature Rev. Genetics 14, 35-48.
-
(2013)
Nature Rev. Genetics
, vol.14
, pp. 35-48
-
-
Altelaar, A.F.1
Munoz, J.2
Heck, A.J.3
-
4
-
-
80855128254
-
Deep proteome and transcriptome mapping of a human cancer cell line
-
Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., and Mann, M. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 7, 548.
-
(2011)
Mol. Syst. Biol
, vol.7
, pp. 548
-
-
Nagaraj, N.1
Wisniewski, J.R.2
Geiger, T.3
Cox, J.4
Kircher, M.5
Kelso, J.6
Pääbo, S.7
Mann, M.8
-
5
-
-
80855128111
-
The quantitative proteome of a human cell line
-
Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., and Aebersold, R. (2011) The quantitative proteome of a human cell line. Mol. Syst. Biol. 7, 549.
-
(2011)
Mol. Syst. Biol
, vol.7
, pp. 549
-
-
Beck, M.1
Schmidt, A.2
Malmstroem, J.3
Claassen, M.4
Ori, A.5
Szymborska, A.6
Herzog, F.7
Rinner, O.8
Ellenberg, J.9
Aebersold, R.10
-
6
-
-
44349113144
-
Estimating the size of the human interactome
-
Stumpf, M. P., Thorne, T., de Silva, E., Stewart, R., An, H. J., Lappe, M., and Wiuf, C. (2008) Estimating the size of the human interactome. Proc. Natl. Acad. Sci. U.S.A. 105, 6959-6964.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 6959-6964
-
-
Stumpf, M.P.1
Thorne, T.2
De Silva, E.3
Stewart, R.4
An, H.J.5
Lappe, M.6
Wiuf, C.7
-
7
-
-
58149305794
-
An empirical framework for binary interactome mapping
-
Venkatesan, K., Rual, J. F., Vazquez, A., Stelzl, U., Lemmens, I., Hirozane- Kishikawa, T., Hao, T., Zenkner, M., Xin, X., Goh, K. I., Yildirim, M. A., Simonis, N., Heinzmann, K., Gebreab, F., Sahalie, J. M., Cevik, S., Simon, C., de Smet, A. S., Dann, E., Smolyar, A., Vinayagam, A., Yu, H., Szeto, D., Borick, H., Dricot, A., Klitgord, N., Murray, R. R., Lin, C., Lalowski, M., Timm, J., Rau, K., Boone, C., Braun, P., Cusick, M. E., Roth, F. P., Hill, D. E., Tavernier, J., Wanker, E. E., Barabá si, A. L., and Vidal, M. (2009) An empirical framework for binary interactome mapping. Nature Meth. 6, 83-90.
-
(2009)
Nature Meth
, vol.6
, pp. 83-90
-
-
Venkatesan, K.1
Rual, J.F.2
Vazquez, A.3
Stelzl, U.4
Lemmens, I.5
Hirozane- Kishikawa, T.6
Hao, T.7
Zenkner, M.8
Xin, X.9
Goh, K.I.10
Yildirim, M.A.11
Simonis, N.12
Heinzmann, K.13
Gebreab, F.14
Sahalie, J.M.15
Cevik, S.16
Simon, C.17
De Smet, A.S.18
Dann, E.19
Smolyar, A.20
Vinayagam, A.21
Yu, H.22
Szeto, D.23
Borick, H.24
Dricot, A.25
Klitgord, N.26
Murray, R.R.27
Lin, C.28
Lalowski, M.29
Timm, J.30
Rau, K.31
Boone, C.32
Braun, P.33
Cusick, M.E.34
Roth, F.P.35
Hill, D.E.36
Tavernier, J.37
Wanker, E.E.38
Barabá Si, A.L.39
Vidal, M.40
more..
-
8
-
-
0024406857
-
A novel genetic system to detect proteinprotein interactions
-
Fields, S., and Song, O. (1989) A novel genetic system to detect proteinprotein interactions. Nature 340, 245-246.
-
(1989)
Nature
, vol.340
, pp. 245-246
-
-
Fields, S.1
Song, O.2
-
9
-
-
34547131554
-
Analysis of protein complexes using mass spectrometry
-
Gingras, A. C., Gstaiger, M., Raught, B., and Aebersold, R. (2007) Analysis of protein complexes using mass spectrometry. Nature Rev. Mol. Cell Biol. 8, 645-654.
-
(2007)
Nature Rev. Mol. Cell Biol
, vol.8
, pp. 645-654
-
-
Gingras, A.C.1
Gstaiger, M.2
Raught, B.3
Aebersold, R.4
-
10
-
-
0037050004
-
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
-
Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A. R., Sassi, H., Nielsen, P. A., Rasmussen, K. J., Andersen, J. R., Johansen, L. E., Hansen, L. H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B. D., Matthiesen, J., Hendrickson, R. C., Gleeson, F., Pawson, T., Moran, M. F., Durocher, D., Mann, M., Hogue, C. W., Figeys, D., and Tyers, M. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
-
(2002)
Nature
, vol.415
, pp. 180-183
-
-
Ho, Y.1
Gruhler, A.2
Heilbut, A.3
Bader, G.D.4
Moore, L.5
Adams, S.L.6
Millar, A.7
Taylor, P.8
Bennett, K.9
Boutilier, K.10
Yang, L.11
Wolting, C.12
Donaldson, I.13
Schandorff, S.14
Shewnarane, J.15
Vo, M.16
Taggart, J.17
Goudreault, M.18
Muskat, B.19
Alfarano, C.20
Dewar, D.21
Lin, Z.22
Michalickova, K.23
Willems, A.R.24
Sassi, H.25
Nielsen, P.A.26
Rasmussen, K.J.27
Andersen, J.R.28
Johansen, L.E.29
Hansen, L.H.30
Jespersen, H.31
Podtelejnikov, A.32
Nielsen, E.33
Crawford, J.34
Poulsen, V.35
Sorensen, B.D.36
Matthiesen, J.37
Hendrickson, R.C.38
Gleeson, F.39
Pawson, T.40
Moran, M.F.41
Durocher, D.42
Mann, M.43
Hogue, C.W.44
Figeys, D.45
Tyers, M.46
more..
-
11
-
-
0037050026
-
Functional organization of the yeast proteome by systematic analysis of protein complexes
-
Gavin, A. C., Bösche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Höfert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147.
-
(2002)
Nature
, vol.415
, pp. 141-147
-
-
Gavin, A.C.1
Bösche, M.2
Krause, R.3
Grandi, P.4
Marzioch, M.5
Bauer, A.6
Schultz, J.7
Rick, J.M.8
Michon, A.M.9
Cruciat, C.M.10
Remor, M.11
Höfert, C.12
Schelder, M.13
Brajenovic, M.14
Ruffner, H.15
Merino, A.16
Klein, K.17
Hudak, M.18
Dickson, D.19
Rudi, T.20
Gnau, V.21
Bauch, A.22
Bastuck, S.23
Huhse, B.24
Leutwein, C.25
Heurtier, M.A.26
Copley, R.R.27
Edelmann, A.28
Querfurth, E.29
Rybin, V.30
Drewes, G.31
Raida, M.32
Bouwmeester, T.33
Bork, P.34
Seraphin, B.35
Kuster, B.36
Neubauer, G.37
Superti-Furga, G.38
more..
-
12
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., Davey, M., Parkinson, J., Greenblatt, J., and Emili, A. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531-537.
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
Peregrín-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
Canadien, V.6
Starostine, A.7
Richards, D.8
Beattie, B.9
Krogan, N.10
Davey, M.11
Parkinson, J.12
Greenblatt, J.13
Emili, A.14
-
13
-
-
33644555054
-
Proteome survey reveals modularity of the yeast cell machinery
-
Gavin, A. C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., Edelmann, A., Heurtier, M. A., Hoffman, V., Hoefert, C., Klein, K., Hudak, M., Michon, A. M., Schelder, M., Schirle, M., Remor, M., Rudi, T., Hooper, S., Bauer, A., Bouwmeester, T., Casari, G., Drewes, G., Neubauer, G., Rick, J. M., Kuster, B., Bork, P., Russell, R. B., and Superti-Furga, G. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631-636.
-
(2006)
Nature
, vol.440
, pp. 631-636
-
-
Gavin, A.C.1
Aloy, P.2
Grandi, P.3
Krause, R.4
Boesche, M.5
Marzioch, M.6
Rau, C.7
Jensen, L.J.8
Bastuck, S.9
Dümpelfeld, B.10
Edelmann, A.11
Heurtier, M.A.12
Hoffman, V.13
Hoefert, C.14
Klein, K.15
Hudak, M.16
Michon, A.M.17
Schelder, M.18
Schirle, M.19
Remor, M.20
Rudi, T.21
Hooper, S.22
Bauer, A.23
Bouwmeester, T.24
Casari, G.25
Drewes, G.26
Neubauer, G.27
Rick, J.M.28
Kuster, B.29
Bork, P.30
Russell, R.B.31
Superti-Furga, G.32
more..
-
14
-
-
33645453254
-
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
-
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A., and Greenblatt, J. F. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643.
-
(2006)
Nature
, vol.440
, pp. 637-643
-
-
Krogan, N.J.1
Cagney, G.2
Yu, H.3
Zhong, G.4
Guo, X.5
Ignatchenko, A.6
Li, J.7
Pu, S.8
Datta, N.9
Tikuisis, A.P.10
Punna, T.11
Peregrín-Alvarez, J.M.12
Shales, M.13
Zhang, X.14
Davey, M.15
Robinson, M.D.16
Paccanaro, A.17
Bray, J.E.18
Sheung, A.19
Beattie, B.20
Richards, D.P.21
Canadien, V.22
Lalev, A.23
Mena, F.24
Wong, P.25
Starostine, A.26
Canete, M.M.27
Vlasblom, J.28
Wu, S.29
Orsi, C.30
Collins, S.R.31
Chandran, S.32
Haw, R.33
Rilstone, J.J.34
Gandi, K.35
Thompson, N.J.36
Musso, G.37
St Onge, P.38
Ghanny, S.39
Lam, M.H.40
Butland, G.41
Altaf-Ul, A.M.42
Kanaya, S.43
Shilatifard, A.44
O'Shea, E.45
Weissman, J.S.46
Ingles, C.J.47
Hughes, T.R.48
Parkinson, J.49
Gerstein, M.50
Wodak, S.J.51
Emili, A.52
Greenblatt, J.F.53
more..
-
15
-
-
33947219266
-
Large-scale mapping of human protein-protein interactions by mass spectrometry
-
Ewing, R. M., Chu, P., Elisma, F., Li, H., Taylor, P., Climie, S., McBroom-Cerajewski, L., Robinson, M. D., O'Connor, L., Li, M., Taylor, R., Dharsee, M., Ho, Y., Heilbut, A., Moore, L., Zhang, S., Ornatsky, O., Bukhman, Y. V., Ethier, M., Sheng, Y., Vasilescu, J., Abu-Farha, M., Lambert, J. P., Duewel, H. S., Stewart, II, Kuehl, B., Hogue, K., Colwill, K., Gladwish, K., Muskat, B., Kinach, R., Adams, S. L., Moran, M. F., Morin, G. B., Topaloglou, T., and Figeys, D. (2007) Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol. Syst. Biol. 3, 89.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 89
-
-
Ewing, R.M.1
Chu, P.2
Elisma, F.3
Li, H.4
Taylor, P.5
Climie, S.6
McBroom-Cerajewski, L.7
Robinson, M.D.8
O'Connor, L.9
Li, M.10
Taylor, R.11
Dharsee, M.12
Ho, Y.13
Heilbut, A.14
Moore, L.15
Zhang, S.16
Ornatsky, O.17
Bukhman, Y.V.18
Ethier, M.19
Sheng, Y.20
Vasilescu, J.21
Abu-Farha, M.22
Lambert, J.P.23
Duewel, H.S.24
Stewart, I.I.25
Kuehl, B.26
Hogue, K.27
Colwill, K.28
Gladwish, K.29
Muskat, B.30
Kinach, R.31
Adams, S.L.32
Moran, M.F.33
Morin, G.B.34
Topaloglou, T.35
Figeys, D.36
more..
-
16
-
-
80155171417
-
A protein complex network of Drosophila melanogaster
-
Guruharsha, K. G., Rual, J. F., Zhai, B., Mintseris, J., Vaidya, P., Vaidya, N., Beekman, C., Wong, C., Rhee, D. Y., Cenaj, O., McKillip, E., Shah, S., Stapleton, M., Wan, K. H., Yu, C., Parsa, B., Carlson, J. W., Chen, X., Kapadia, B., VijayRaghavan, K., Gygi, S. P., Celniker, S. E., Obar, R. A., and Artavanis-Tsakonas, S. (2011) A protein complex network of Drosophila melanogaster. Cell 147, 690-703.
-
(2011)
Cell
, vol.147
, pp. 690-703
-
-
Guruharsha, K.G.1
Rual, J.F.2
Zhai, B.3
Mintseris, J.4
Vaidya, P.5
Vaidya, N.6
Beekman, C.7
Wong, C.8
Rhee, D.Y.9
Cenaj, O.10
McKillip, E.11
Shah, S.12
Stapleton, M.13
Wan, K.H.14
Yu, C.15
Parsa, B.16
Carlson, J.W.17
Chen, X.18
Kapadia, B.19
VijayRaghavan, K.20
Gygi, S.P.21
Celniker, S.E.22
Obar, R.A.23
Artavanis-Tsakonas, S.24
more..
-
17
-
-
79957575162
-
Analysis of the human endogenous coregulator complexome
-
Malovannaya, A., Lanz, R. B., Jung, S. Y., Bulynko, Y., Le, N. T., Chan, D. W., Ding, C., Shi, Y., Yucer, N., Krenciute, G., Kim, B. J., Li, C., Chen, R., Li, W., Wang, Y., O'Malley, B. W., and Qin, J. (2011) Analysis of the human endogenous coregulator complexome. Cell 145, 787-799.
-
(2011)
Cell
, vol.145
, pp. 787-799
-
-
Malovannaya, A.1
Lanz, R.B.2
Jung, S.Y.3
Bulynko, Y.4
Le, N.T.5
Chan, D.W.6
Ding, C.7
Shi, Y.8
Yucer, N.9
Krenciute, G.10
Kim, B.J.11
Li, C.12
Chen, R.13
Li, W.14
Wang, Y.15
O'Malley, B.W.16
Qin, J.17
-
18
-
-
79551517793
-
Recent advances in charting protein-protein interaction: Mass spectrometry-based approaches
-
Gavin, A. C., Maeda, K., and Kühner, S. (2011) Recent advances in charting protein-protein interaction: Mass spectrometry-based approaches. Curr. Opin. Biotechnol. 22, 42-49.
-
(2011)
Curr. Opin. Biotechnol
, vol.22
, pp. 42-49
-
-
Gavin, A.C.1
Maeda, K.2
Kühner, S.3
-
19
-
-
49549121813
-
High confidence determination of specific protein-protein interactions using quantitative mass spectrometry
-
Vermeulen, M., Hubner, N. C., and Mann, M. (2008) High confidence determination of specific protein-protein interactions using quantitative mass spectrometry. Curr. Opin. Biotechnol. 19, 331-337.
-
(2008)
Curr. Opin. Biotechnol
, vol.19
, pp. 331-337
-
-
Vermeulen, M.1
Hubner, N.C.2
Mann, M.3
-
20
-
-
79959211995
-
Analyzing protein-protein interactions by quantitative mass spectrometry
-
Paul, F. E., Hosp, F., and Selbach, M. (2011) Analyzing protein-protein interactions by quantitative mass spectrometry. Methods 54, 387-395.
-
(2011)
Methods
, vol.54
, pp. 387-395
-
-
Paul, F.E.1
Hosp, F.2
Selbach, M.3
-
21
-
-
85017746781
-
Accurate protein complex retrieval by affinity enrichment MS rather than affinity purification MS
-
Keilhauer, E. C., Hein, M. Y., and Mann, M. (2014) Accurate protein complex retrieval by affinity enrichment MS rather than affinity purification MS. Mol. Cell. Proteomics.
-
(2014)
Mol. Cell. Proteomics
-
-
Keilhauer, E.C.1
Hein, M.Y.2
Mann, M.3
-
22
-
-
0037337310
-
A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling
-
Blagoev, B., Kratchmarova, I., Ong, S. E., Nielsen, M., Foster, L. J., and Mann, M. (2003) A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nature Biotechnol. 21, 315-318.
-
(2003)
Nature Biotechnol
, vol.21
, pp. 315-318
-
-
Blagoev, B.1
Kratchmarova, I.2
Ong, S.E.3
Nielsen, M.4
Foster, L.J.5
Mann, M.6
-
23
-
-
34948875686
-
Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors
-
Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S., Boesche, M., Hobson, S., Mathieson, T., Perrin, J., Raida, M., Rau, C., Reader, V., Sweetman, G., Bauer, A., Bouwmeester, T., Hopf, C., Kruse, U., Neubauer, G., Ramsden, N., Rick, J., Kuster, B., and Drewes, G. (2007) Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nature Biotechnol. 25, 1035-1044.
-
(2007)
Nature Biotechnol
, vol.25
, pp. 1035-1044
-
-
Bantscheff, M.1
Eberhard, D.2
Abraham, Y.3
Bastuck, S.4
Boesche, M.5
Hobson, S.6
Mathieson, T.7
Perrin, J.8
Raida, M.9
Rau, C.10
Reader, V.11
Sweetman, G.12
Bauer, A.13
Bouwmeester, T.14
Hopf, C.15
Kruse, U.16
Neubauer, G.17
Ramsden, N.18
Rick, J.19
Kuster, B.20
Drewes, G.21
more..
-
24
-
-
33947182552
-
An integrated mass spectrometric and computational framework for the analysis of protein interaction networks
-
Rinner, O., Mueller, L. N., Hubálek, M., Muller, M., Gstaiger, M., and Aebersold, R. (2007) An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nature Biotechnol. 25, 345-352.
-
(2007)
Nature Biotechnol
, vol.25
, pp. 345-352
-
-
Rinner, O.1
Mueller, L.N.2
Hubálek, M.3
Muller, M.4
Gstaiger, M.5
Aebersold, R.6
-
25
-
-
43849110454
-
Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes
-
Mousson, F., Kolkman, A., Pijnappel, W. W., Timmers, H. T., and Heck, A. J. (2008) Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes. Mol. Cell. Proteomics 7, 845-852.
-
(2008)
Mol. Cell. Proteomics
, vol.7
, pp. 845-852
-
-
Mousson, F.1
Kolkman, A.2
Pijnappel, W.W.3
Timmers, H.T.4
Heck, A.J.5
-
26
-
-
64649100982
-
Host cell interactome of tyrosine-phosphorylated bacterial proteins
-
Selbach, M., Paul, F. E., Brandt, S., Guye, P., Daumke, O., Backert, S., Dehio, C., and Mann, M. (2009) Host cell interactome of tyrosine-phosphorylated bacterial proteins. Cell Host Microbe 5, 397-403.
-
(2009)
Cell Host Microbe
, vol.5
, pp. 397-403
-
-
Selbach, M.1
Paul, F.E.2
Brandt, S.3
Guye, P.4
Daumke, O.5
Backert, S.6
Dehio, C.7
Mann, M.8
-
27
-
-
77956643239
-
Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers
-
Vermeulen, M., Eberl, H. C., Matarese, F., Marks, H., Denissov, S., Butter, F., Lee, K. K., Olsen, J. V., Hyman, A. A., Stunnenberg, H. G., and Mann, M. (2010) Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142, 967-980.
-
(2010)
Cell
, vol.142
, pp. 967-980
-
-
Vermeulen, M.1
Eberl, H.C.2
Matarese, F.3
Marks, H.4
Denissov, S.5
Butter, F.6
Lee, K.K.7
Olsen, J.V.8
Hyman, A.A.9
Stunnenberg, H.G.10
Mann, M.11
-
28
-
-
84865718193
-
Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses
-
McAlister, G. C., Huttlin, E. L., Haas, W., Ting, L., Jedrychowski, M. P., Rogers, J. C., Kuhn, K., Pike, I., Grothe, R. A., Blethrow, J. D., and Gygi, S. P. (2012) Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. Anal. Chem. 84, 7469-7478.
-
(2012)
Anal. Chem
, vol.84
, pp. 7469-7478
-
-
McAlister, G.C.1
Huttlin, E.L.2
Haas, W.3
Ting, L.4
Jedrychowski, M.P.5
Rogers, J.C.6
Kuhn, K.7
Pike, I.8
Grothe, R.A.9
Blethrow, J.D.10
Gygi, S.P.11
-
29
-
-
84865454296
-
High-resolution enabled TMT 8-plexing
-
Werner, T., Becher, I., Sweetman, G., Doce, C., Savitski, M. M., and Bantscheff, M. (2012) High-resolution enabled TMT 8-plexing. Anal. Chem. 84, 7188-7194.
-
(2012)
Anal. Chem
, vol.84
, pp. 7188-7194
-
-
Werner, T.1
Becher, I.2
Sweetman, G.3
Doce, C.4
Savitski, M.M.5
Bantscheff, M.6
-
30
-
-
76149102921
-
An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies
-
Baker, E. S., Livesay, E. A., Orton, D. J., Moore, R. J., Danielson, W. F. 3rd, Prior, D. C., Ibrahim, Y. M., LaMarche, B. L., Mayampurath, A. M., Schepmoes, A. A., Hopkins, D. F., Tang, K., Smith, R. D., and Belov, M. E. (2010) An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J. Proteome Res. 9, 997-1006.
-
(2010)
J. Proteome Res
, vol.9
, pp. 997-1006
-
-
Baker, E.S.1
Livesay, E.A.2
Orton, D.J.3
Moore, R.J.4
Danielson, W.F.5
Prior, D.C.6
Ibrahim, Y.M.7
LaMarche, B.L.8
Mayampurath, A.M.9
Schepmoes, A.A.10
Hopkins, D.F.11
Tang, K.12
Smith, R.D.13
Belov, M.E.14
-
31
-
-
84915748592
-
Integrated solid-phase extraction-capillary liquid chromatography (speLC) interfaced to ESI-MS/MS for fast characterization and quantification of protein and proteomes
-
Falkenby, L. G., Such-Sanmartin, G., Larsen, M. R., Vorm, O., Bache, N., and Jensen, O. N. (2014) Integrated solid-phase extraction-capillary liquid chromatography (speLC) interfaced to ESI-MS/MS for fast characterization and quantification of protein and proteomes. J. Proteome Res. 13, 6169-6175.
-
(2014)
J. Proteome Res
, vol.13
, pp. 6169-6175
-
-
Falkenby, L.G.1
Such-Sanmartin, G.2
Larsen, M.R.3
Vorm, O.4
Bache, N.5
Jensen, O.N.6
-
32
-
-
84922665110
-
Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS system
-
Binai, N. A., Marino, F., Soendergaard, P., Bache, N., Mohammed, S., and Heck, A. J. (2015) Rapid analyses of proteomes and interactomes using an integrated solid-phase extraction-liquid chromatography-MS/MS system. J. Proteome Res. 14, 977-985.
-
(2015)
J. Proteome Res
, vol.14
, pp. 977-985
-
-
Binai, N.A.1
Marino, F.2
Soendergaard, P.3
Bache, N.4
Mohammed, S.5
Heck, A.J.6
-
33
-
-
80051624900
-
Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation
-
M110.003699
-
Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Fröhlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell. Proteomics 10, M110.003699.
-
(2011)
Mol. Cell. Proteomics
, pp. 10
-
-
Thakur, S.S.1
Geiger, T.2
Chatterjee, B.3
Bandilla, P.4
Fröhlich, F.5
Cox, J.6
Mann, M.7
-
34
-
-
84925881208
-
The Q Exactive HF, a benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer
-
Scheltema, R. A., Hauschild, J. P., Lange, O., Hornburg, D., Denisov, E., Damoc, E., Kuehn, A., Makarov, A., and Mann, M. (2014) The Q Exactive HF, a benchtop mass spectrometer with a pre-filter, high-performance quadrupole and an ultra-high-field Orbitrap analyzer. Mol. Cell. Proteomics 13, 3698-3708.
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 3698-3708
-
-
Scheltema, R.A.1
Hauschild, J.P.2
Lange, O.3
Hornburg, D.4
Denisov, E.5
Damoc, E.6
Kuehn, A.7
Makarov, A.8
Mann, M.9
-
35
-
-
0035387847
-
High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry
-
Shen, Y., Tolić, N., Zhao, R., Pasa-Tolić, L., Li, L., Berger, S. J., Harkewicz, R., Anderson, G. A., Belov, M. E., and Smith, R. D. (2001) High-throughput proteomics using high-efficiency multiple-capillary liquid chromatography with on-line high-performance ESI FTICR mass spectrometry. Anal. Chem. 73, 3011-3021.
-
(2001)
Anal. Chem
, vol.73
, pp. 3011-3021
-
-
Shen, Y.1
Tolić, N.2
Zhao, R.3
Pasa-Tolić, L.4
Li, L.5
Berger, S.J.6
Harkewicz, R.7
Anderson, G.A.8
Belov, M.E.9
Smith, R.D.10
-
36
-
-
10744224779
-
An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics
-
Belov, M. E., Anderson, G. A., Wingerd, M. A., Udseth, H. R., Tang, K., Prior, D. C., Swanson, K. R., Buschbach, M. A., Strittmatter, E. F., Moore, R. J., and Smith, R. D. (2004) An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics. J. Amer. Soc. Mass Spec. 15, 212-232.
-
(2004)
J. Amer. Soc. Mass Spec
, vol.15
, pp. 212-232
-
-
Belov, M.E.1
Anderson, G.A.2
Wingerd, M.A.3
Udseth, H.R.4
Tang, K.5
Prior, D.C.6
Swanson, K.R.7
Buschbach, M.A.8
Strittmatter, E.F.9
Moore, R.J.10
Smith, R.D.11
-
37
-
-
29644439120
-
Multiplex multidimensional nanoLC-MS system for targeted proteomic analyses
-
Bonneil, E., Tessier, S., Carrier, A., and Thibault, P. (2005) Multiplex multidimensional nanoLC-MS system for targeted proteomic analyses. Electrophoresis 26, 4575-4589.
-
(2005)
Electrophoresis
, vol.26
, pp. 4575-4589
-
-
Bonneil, E.1
Tessier, S.2
Carrier, A.3
Thibault, P.4
-
38
-
-
41149134523
-
Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses
-
Livesay, E. A., Tang, K., Taylor, B. K., Buschbach, M. A., Hopkins, D. F., LaMarche, B. L., Zhao, R., Shen, Y., Orton, D. J., Moore, R. J., Kelly, R. T., Udseth, H. R., and Smith, R. D. (2008) Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. Anal. Chem. 80, 294-302.
-
(2008)
Anal. Chem
, vol.80
, pp. 294-302
-
-
Livesay, E.A.1
Tang, K.2
Taylor, B.K.3
Buschbach, M.A.4
Hopkins, D.F.5
LaMarche, B.L.6
Zhao, R.7
Shen, Y.8
Orton, D.J.9
Moore, R.J.10
Kelly, R.T.11
Udseth, H.R.12
Smith, R.D.13
-
39
-
-
84890092602
-
Dual LC-MS platform for high-throughput proteome analysis
-
Orton, D. J., Wall, M. J., and Doucette, A. A. (2013) Dual LC-MS platform for high-throughput proteome analysis. J. Proteome Res. 12, 5963-5970.
-
(2013)
J. Proteome Res
, vol.12
, pp. 5963-5970
-
-
Orton, D.J.1
Wall, M.J.2
Doucette, A.A.3
-
40
-
-
77954237882
-
Network organization of the human autophagy system
-
Behrends, C., Sowa, M. E., Gygi, S. P., and Harper, J. W. (2010) Network organization of the human autophagy system. Nature 466, 68-76.
-
(2010)
Nature
, vol.466
, pp. 68-76
-
-
Behrends, C.1
Sowa, M.E.2
Gygi, S.P.3
Harper, J.W.4
-
41
-
-
84888858053
-
Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system
-
Collins, B. C., Gillet, L. C., Rosenberger, G., Röst, H. L., Vichalkovski, A., Gstaiger, M., and Aebersold, R. (2013) Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system. Nature Meth. 10, 1246-1253.
-
(2013)
Nature Meth
, vol.10
, pp. 1246-1253
-
-
Collins, B.C.1
Gillet, L.C.2
Rosenberger, G.3
Röst, H.L.4
Vichalkovski, A.5
Gstaiger, M.6
Aebersold, R.7
-
42
-
-
84873401531
-
Using guanidine-hydrochloride for fast and efficient protein digestion and single-step affinity-purification mass spectrometry
-
Poulsen, J. W., Madsen, C. T., Young, C., Poulsen, F. M., and Nielsen, M. L. (2013) Using guanidine-hydrochloride for fast and efficient protein digestion and single-step affinity-purification mass spectrometry. J. Proteome Res. 12, 1020-1030.
-
(2013)
J. Proteome Res
, vol.12
, pp. 1020-1030
-
-
Poulsen, J.W.1
Madsen, C.T.2
Young, C.3
Poulsen, F.M.4
Nielsen, M.L.5
-
43
-
-
0142184341
-
Global analysis of protein localization in budding yeast
-
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425, 686-691.
-
(2003)
Nature
, vol.425
, pp. 686-691
-
-
Huh, W.K.1
Falvo, J.V.2
Gerke, L.C.3
Carroll, A.S.4
Howson, R.W.5
Weissman, J.S.6
O'Shea, E.K.7
-
44
-
-
0037317228
-
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics
-
Rappsilber, J., Ishihama, Y., and Mann, M. (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663-670.
-
(2003)
Anal. Chem
, vol.75
, pp. 663-670
-
-
Rappsilber, J.1
Ishihama, Y.2
Mann, M.3
-
45
-
-
84861795226
-
SprayQc: A real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components
-
Scheltema, R. A., and Mann, M. (2012) SprayQc: A real-time LC-MS/MS quality monitoring system to maximize uptime using off the shelf components. J. Proteome Res. 11, 3458-3466.
-
(2012)
J. Proteome Res
, vol.11
, pp. 3458-3466
-
-
Scheltema, R.A.1
Mann, M.2
-
46
-
-
57449099865
-
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
-
Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnol. 26, 1367-1372.
-
(2008)
Nature Biotechnol
, vol.26
, pp. 1367-1372
-
-
Cox, J.1
Mann, M.2
-
47
-
-
79953701087
-
Andromeda: A peptide search engine integrated into the MaxQuant environment
-
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: A peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805.
-
(2011)
J. Proteome Res
, vol.10
, pp. 1794-1805
-
-
Cox, J.1
Neuhauser, N.2
Michalski, A.3
Scheltema, R.A.4
Olsen, J.V.5
Mann, M.6
-
48
-
-
84907197082
-
Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
-
Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., and Mann, M. (2014) Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513-2526.
-
(2014)
Mol. Cell. Proteomics
, vol.13
, pp. 2513-2526
-
-
Cox, J.1
Hein, M.Y.2
Luber, C.A.3
Paron, I.4
Nagaraj, N.5
Mann, M.6
-
49
-
-
0030305457
-
R: A language for data analysis and graphics
-
Ihaka, R., and Gentleman, R. (1996) R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5, 299-314.
-
(1996)
J. Comput. Graph. Stat.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
51
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher, V. G., Tibshirani, R., and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. U.S.A. 98, 5116-5121.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
52
-
-
79956322553
-
Global quantification of mammalian gene expression control
-
Schwä nhausser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., and Selbach, M. (2011) Global quantification of mammalian gene expression control. Nature 473, 337-342.
-
(2011)
Nature
, vol.473
, pp. 337-342
-
-
Schwä Nhausser, B.1
Busse, D.2
Li, N.3
Dittmar, G.4
Schuchhardt, J.5
Wolf, J.6
Chen, W.7
Selbach, M.8
-
53
-
-
84895538371
-
Minimal, encapsulated proteomic-sample processing applied to copynumber estimation in eukaryotic cells
-
Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., and Mann, M. (2014) Minimal, encapsulated proteomic-sample processing applied to copynumber estimation in eukaryotic cells. Nature Meth. 11, 319-324.
-
(2014)
Nature Meth
, vol.11
, pp. 319-324
-
-
Kulak, N.A.1
Pichler, G.2
Paron, I.3
Nagaraj, N.4
Mann, M.5
-
54
-
-
0033231625
-
Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains
-
Cairns, B. R., Schlichter, A., Erdjument-Bromage, H., Tempst, P., Kornberg, R. D., and Winston, F. (1999) Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Molecular Cell 4, 715-723.
-
(1999)
Molecular Cell
, vol.4
, pp. 715-723
-
-
Cairns, B.R.1
Schlichter, A.2
Erdjument-Bromage, H.3
Tempst, P.4
Kornberg, R.D.5
Winston, F.6
-
55
-
-
84857136872
-
The two different isoforms of the RSC chromatin remodeling complex play distinct roles in DNA damage responses
-
Chambers, A. L., Brownlee, P. M., Durley, S. C., Beacham, T., Kent, N. A., and Downs, J. A. (2012) The two different isoforms of the RSC chromatin remodeling complex play distinct roles in DNA damage responses. PloS One 7, e32016.
-
(2012)
PloS One
, vol.7
, pp. e32016
-
-
Chambers, A.L.1
Brownlee, P.M.2
Durley, S.C.3
Beacham, T.4
Kent, N.A.5
Downs, J.A.6
-
56
-
-
82355165009
-
Identifying cellular targets of small-molecule probes and drugs with biochemical enrichment and SILAC
-
Ong, S. E., Li, X., Schenone, M., Schreiber, S. L., and Carr, S. A. (2012) Identifying cellular targets of small-molecule probes and drugs with biochemical enrichment and SILAC. Meth. Mol. Biol. 803, 129-140.
-
(2012)
Meth. Mol. Biol.
, vol.803
, pp. 129-140
-
-
Ong, S.E.1
Li, X.2
Schenone, M.3
Schreiber, S.L.4
Carr, S.A.5
-
57
-
-
84859385670
-
High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis
-
Yang, F., Shen, Y., Camp, D. G. 2nd, and Smith, R. D. (2012) High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev. Proteomics 9, 129-134.
-
(2012)
Expert Rev. Proteomics
, vol.9
, pp. 129-134
-
-
Yang, F.1
Shen, Y.2
Camp, D.G.3
Smith, R.D.4
-
58
-
-
84915774615
-
Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer
-
Kelstrup, C. D., Jersie-Christensen, R. R., Batth, T. S., Arrey, T. N., Kuehn, A., Kellmann, M., and Olsen, J. V. (2014) Rapid and deep proteomes by faster sequencing on a benchtop quadrupole ultra-high-field Orbitrap mass spectrometer. J. Proteome Res. 13, 6187-6195.
-
(2014)
J. Proteome Res
, vol.13
, pp. 6187-6195
-
-
Kelstrup, C.D.1
Jersie-Christensen, R.R.2
Batth, T.S.3
Arrey, T.N.4
Kuehn, A.5
Kellmann, M.6
Olsen, J.V.7
-
59
-
-
84891796097
-
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
-
Vizcaíno, J. A., Deutsch, E. W., Wang, R., Csordas, A., Reisinger, F., Rios, D., Dianes, J. A., Sun, Z., Farrah, T., Bandeira, N., Binz, P. A., Xenarios, I., Eisenacher, M., Mayer, G., Gatto, L., Campos, A., Chalkley, R. J., Kraus, H. J., Albar, J. P., Martinez-Bartolomé, S., Apweiler, R., Omenn, G. S., Martens, L., Jones, A. R., and Hermjakob, H. (2014) ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnol. 32, 223-226.
-
(2014)
Nature Biotechnol
, vol.32
, pp. 223-226
-
-
Vizcaíno, J.A.1
Deutsch, E.W.2
Wang, R.3
Csordas, A.4
Reisinger, F.5
Rios, D.6
Dianes, J.A.7
Sun, Z.8
Farrah, T.9
Bandeira, N.10
Binz, P.A.11
Xenarios, I.12
Eisenacher, M.13
Mayer, G.14
Gatto, L.15
Campos, A.16
Chalkley, R.J.17
Kraus, H.J.18
Albar, J.P.19
Martinez-Bartolomé, S.20
Apweiler, R.21
Omenn, G.S.22
Martens, L.23
Jones, A.R.24
Hermjakob, H.25
more..
-
60
-
-
84874762979
-
The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013
-
Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Perez-Riverol, Y., Reisinger, F., Rios, D., Wang, R., and Hermjakob, H. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-D1069.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D1063-D1069
-
-
Vizcaíno, J.A.1
Côté, R.G.2
Csordas, A.3
Dianes, J.A.4
Fabregat, A.5
Foster, J.M.6
Griss, J.7
Alpi, E.8
Birim, M.9
Contell, J.10
O'Kelly, G.11
Schoenegger, A.12
Ovelleiro, D.13
Perez-Riverol, Y.14
Reisinger, F.15
Rios, D.16
Wang, R.17
Hermjakob, H.18
|